We studied the transformation of a middle-to-late Holocene forested ecosystem using the highly indicative remains of land snails. The study areas were sandstone landscapes of northern Bohemia (Czech Republic) that provide extremely rich terrestrial fossil records. As far as we know, nowhere else in the world does such a type of sedimentary environment provide Holocene records of snail shells. Currently, these sandstone landscapes are covered by low productivity coniferous forests with very low species pools. In sharp contrast, in the middle Holocene, they were dominated by species-rich productive woodland communities. Such ecosystems were then supported by a favourable warm and wet climate and by nutrient-rich, calcareous substrata formed of late Pleistocene aeolian dust (loess). A radical transformation of this temporal ecological equilibrium began in the third millennium BC. Over the next millennia, the species-rich canopy forest mollusc assemblages almost completely disappeared, together with calciphilous rock dwellers. The main driving force of this transformation was gradual soil leaching that resulted in the loss of calcium carbonate and principal nutrients (like P and N) and subsequent ecosystem retrogression. Synergistically with this background trend, the unstable climatic regime of the late Holocene, along with long-term anthropogenic pressure that peaked for the first time during the late Bronze Age, accelerated the transformation.